Trillions of bacteria call the human gut home. The bugs affect not only our digestion but our hormones and immune systems, too. Now researchers show most of the microbes that colonize mammals’ guts pass down from generation to generation. The few that don’t tend to be the kind that makes us sick. The discovery suggests pathogens evolved to spread between individuals instead of through inheritance.

Generation to Generation

Andrew Moeller, an evolutionary biologist at Cornell University in Ithaca, New York, who led the new research, wondered whether gut microbes that cause disease are specially tuned to spread between unrelated individuals through social interactions or shared environments. To find out, Moeller and his team captured two populations of wild mice. One came from the hot deserts of Tucson, Arizona. The other came from the northern climes of Edmonton, Alberta in Canada. Both populations lived in the same room in the upstate New York laboratory. The researchers then bred the two populations separately for 11 generations and assessed the communities of microbes living in each groups’ guts.

“We found that gut bacteria tended to be inherited… or transmitted,” Moeller said.

The team discovered that individuals in each of the two populations retained most of the same microbes, meaning gut bug communities are likely passed down from generation to generation. Only a few kinds of gut bugs were passed between the populations, Moeller and his team report Thursday in the journal Science. And those were bad kind.

“We found that gut bacterial genera that were horizontally transmitted in our experiment in mice most commonly cause food-borne illness and healthcare associated infections in humans in the United States,” Moeller said. “These results suggest that bacterial pathogens in the gut microbiome tend to emerge from groups of bacteria that are horizontally transmitted.”

Microbiome Maturation

Although the gut microbiome might appear stable over generations, two new long-term studies in humans find that it takes a few years for our microbial communities to mature.

In the first year of life, a few dominant species rule the infant’s gut microbiome, according to a longitudinal analysis of nearly 1,000 mostly white, non-Hispanic children published Wednesday in the journal Nature Letters. A bacterium known as B. longum that helps babies use human milk grew predominantly in the guts of breastfed infants, for example. Still, each baby’s gut community was highly individualized the authors reported.

Another study published in the same issue showed infant’s gut microbiomes go through three distinct phases after birth: first a developmental phase and then a transitional phase until finally it matures into a stable phase around three to four years of age.

“It seems many of the same gut bacterial genera that are inherited in our experiment are also inherited in humans,” said Moeller in response to the human studies. “I suspect the transmission modes of gut bacteria genera may be fairly consistent across mammalian species.”